Root rots are a major biotic factor impacting negatively on the production of common beans (Phaseolus vulgaris L.) in smallholder farming systems. The search for revamping approaches toward the management of root rots is welcome. Therefore, this study evaluated the effect of intercropping and legume diversification on the intensity of the root rot disease complex of common beans in Western Kenya. Farm saved bean seeds of GLP2 (Rose coco) bean variety and seeds of varieties KATX56 and KK8 sourced from the local market and Kenya Agricultural and Livestock Research Organization (KALRO), respectively, and subsequently planted on ten farms. The treatments of this study consisted of intercrops of each of the three bean varieties with maize compared to sole bean crops. Two legumes, cowpea and groundnuts, variety K80 and Red Valencia, respectively were incorporated to achieve diversification. Data was collected on the population of soil-borne fungal pathogens causing root rots before planting, at two and four weeks after emergence; plant stand and root rot intensity. Fusarium solani, Fusarium oxysporum, Macrophomina phaseolina, Pythium spp., and Rhizoctonia solani were isolated from both sample soils and symptomatic bean plants. Intercrops and diversification cropping systems resulted in a significant (p ≤ 0.05) decrease in the incidence of root rot pathogens and intensity of root rot. The results showed that bean sole cropping is more prone to root rots than when intercropped with maize and other legumes. These two cropping systems, intercropping and diversification are effective approaches for the suppression of bean root rot pathogens.